Experiment set1H20 for Shewanella sp. ANA-3

Sodium propionate carbon source

Group: carbon source
Media: ShewMM_noCarbon + Sodium propionate (20 mM), pH=7
Culturing: ANA3_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.4 generations
By: Jake on 2/12/2014
Media components: 1.5 g/L Ammonium chloride, 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 16 genes in this experiment

For carbon source Sodium propionate in Shewanella sp. ANA-3

For carbon source Sodium propionate across organisms

SEED Subsystems

Subsystem	#Specific
CO2 uptake, carboxysome	2
Acetyl-CoA fermentation to Butyrate	1
Butanol Biosynthesis	1
Hemin transport system	1
Isoleucine degradation	1
Polyhydroxybutyrate metabolism	1
Purine Utilization	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Restriction-Modification System	1
Ton and Tol transport systems	1
Valine degradation	1
n-Phenylalkanoic acid degradation	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Fatty acid metabolism
• Geraniol degradation
• Arginine and proline metabolism
• Tryptophan metabolism
• Butanoate metabolism
• Fatty acid elongation in mitochondria
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Benzoate degradation via CoA ligation
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of plant hormones
• Bile acid biosynthesis
• Purine metabolism
• Glutamate metabolism
• Lysine biosynthesis
• beta-Alanine metabolism
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Propanoate metabolism
• Folate biosynthesis
• Nitrogen metabolism
• Biosynthesis of unsaturated fatty acids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
fatty acid β-oxidation III (unsaturated, odd number)	1	1	1
L-glutamine biosynthesis I	1	1	1
benzoyl-CoA biosynthesis	3	3	2
fatty acid β-oxidation IV (unsaturated, even number)	5	4	3
fatty acid β-oxidation I (generic)	7	6	4
ammonia assimilation cycle II	2	2	1
oleate β-oxidation (thioesterase-dependent, yeast)	2	2	1
ammonia assimilation cycle I	2	2	1
putrescine degradation V	2	1	1
putrescine degradation I	2	1	1
oleate β-oxidation	35	32	16
adipate degradation	5	4	2
fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent)	5	3	2
fatty acid β-oxidation II (plant peroxisome)	5	3	2
glutaryl-CoA degradation	5	3	2
adipate biosynthesis	5	3	2
pyruvate fermentation to hexanol (engineered)	11	7	4
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	4
2-methyl-branched fatty acid β-oxidation	14	9	5
fatty acid salvage	6	6	2
superpathway of ammonia assimilation (plants)	3	3	1
ammonia assimilation cycle III	3	3	1
pyruvate fermentation to butanol II (engineered)	6	5	2
L-isoleucine degradation I	6	4	2
L-aspartate degradation III (anaerobic)	3	2	1
oleate β-oxidation (reductase-dependent, yeast)	3	2	1
putrescine degradation IV	3	2	1
valproate β-oxidation	9	5	3
methyl ketone biosynthesis (engineered)	6	3	2
propanoate fermentation to 2-methylbutanoate	6	3	2
L-aspartate degradation II (aerobic)	3	1	1
pyruvate fermentation to butanoate	7	3	2
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	2
benzoyl-CoA degradation I (aerobic)	7	2	2
L-valine degradation I	8	6	2
superpathway of ornithine degradation	8	6	2
putrescine degradation II	4	3	1
pyruvate fermentation to butanol I	8	4	2
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	1	1
L-arginine degradation VIII (arginine oxidase pathway)	4	1	1
oleate β-oxidation (isomerase-dependent, yeast)	4	1	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	2
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	2
phenylacetate degradation I (aerobic)	9	2	2
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	5	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	4	2
3-phenylpropanoate degradation	10	4	2
4-hydroxybenzoate biosynthesis III (plants)	5	2	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	2
superpathway of phenylethylamine degradation	11	3	2
L-glutamate degradation VII (to butanoate)	12	4	2
6-gingerol analog biosynthesis (engineered)	6	2	1
superpathway of L-arginine and L-ornithine degradation	13	8	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	6	2
L-glutamate and L-glutamine biosynthesis	7	6	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
Spodoptera littoralis pheromone biosynthesis	22	4	3
L-tryptophan degradation III (eukaryotic)	15	4	2
glycerol degradation to butanol	16	10	2
2-methylpropene degradation	8	2	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	3	2
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	2
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	3	2
3-hydroxypropanoate/4-hydroxybutanate cycle	18	7	2
toluene degradation VI (anaerobic)	18	3	2
L-arginine biosynthesis II (acetyl cycle)	10	9	1
methyl tert-butyl ether degradation	10	2	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	6	1
gallate degradation III (anaerobic)	11	3	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	3	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	3	1
androstenedione degradation I (aerobic)	25	6	2
platensimycin biosynthesis	26	6	2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
1-butanol autotrophic biosynthesis (engineered)	27	21	2
androstenedione degradation II (anaerobic)	27	4	2
superpathway of testosterone and androsterone degradation	28	6	2
superpathway of cholesterol degradation I (cholesterol oxidase)	42	8	3
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	8	3
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	2	1
superpathway of cholesterol degradation III (oxidase)	49	4	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	21	1